def run(self, data):
        logging.debug('Worker ID: ' + str(self.id) + ' Building finder '
                                                     '=========')
        logging.debug(data)

        kernel_file_url = data['kernel_url']
        network_file_url = data['network_url']
        query = data['query']

        # Check finder exists or not
        if kernel_file_url in self.__finders.keys():
            logging.debug('Kernel found.  No need to create finder')
            finder = self.__finders[kernel_file_url]
        else:
            logging.debug('Building Finder...')
            generator = KernelGenerator()
            kernel = generator.create_kernel_from_file(kernel_file_url)
            network = util.read_sif(network_file_url)
            finder = SubNetworkFinder(kernel=kernel, network=network)
            self.__finders[kernel_file_url] = finder
            logging.debug('Building Finder... Done!')

        # Now find subnet
        logging.debug('******** Query: ' + str(query))
        subnetwork = finder.get_sub_network(query)
        logging.debug('========== Sub Network found: Size = ' + str(len(
            subnetwork)))

        return subnetwork
Пример #2
0
    def run(self, data):
        logging.debug('Worker ID: ' + str(self.id) + ' Building finder '
                      '=========')
        logging.debug(data)

        kernel_file_url = data['kernel_url']
        network_file_url = data['network_url']
        query = data['query']

        # Check finder exists or not
        if kernel_file_url in self.__finders.keys():
            logging.debug('Kernel found.  No need to create finder')
            finder = self.__finders[kernel_file_url]
        else:
            logging.debug('Building Finder...')
            generator = KernelGenerator()
            kernel = generator.create_kernel_from_file(kernel_file_url)
            network = util.read_sif(network_file_url)
            finder = SubNetworkFinder(kernel=kernel, network=network)
            self.__finders[kernel_file_url] = finder
            logging.debug('Building Finder... Done!')

        # Now find subnet
        logging.debug('******** Query: ' + str(query))
        subnetwork = finder.get_sub_network(query)
        logging.debug('========== Sub Network found: Size = ' +
                      str(len(subnetwork)))

        return subnetwork
Пример #3
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    def test_sif2cx(self):
        import hdsubnetfinder.subnetwork.network_util as util
        triples = util.read_sif(small_network)
        cx = util.sif2cx(triples)
        print(json.dumps(cx, indent=4))

        self.assertEqual(list, type(cx))
Пример #4
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    def test_read_sif(self):
        import hdsubnetfinder.subnetwork.network_util as util
        df = pd.read_csv(small_network, sep='\t', names=['source', 'interaction', 'target'])
        print(df.shape)

        triples = util.read_sif(small_network)
        self.assertIsNotNone(triples)
        self.assertEqual(df.shape[0], len(triples))
Пример #5
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    def test_find_sub_network2(self):
        print('\n---------- Sub Network Finder tests 2 start -----------\n')

        from hdsubnetfinder.subnetwork.sub_network_finder import SubNetworkFinder
        import hdsubnetfinder.subnetwork.network_util as util
        from hdsubnetfinder.kernel.kernel_generator import KernelGenerator

        generator = KernelGenerator()
        small_kernel = generator.create_kernel(network_url=NETWORK_URL)
        small_sif = util.read_sif(file_url=NETWORK_URL)

        finder = SubNetworkFinder(network=small_sif, kernel=small_kernel)

        identifiers = ["NRAS", "KRAS", "MAPK1"]

        result = finder.get_sub_network(identifiers)
        self.assertIsNotNone(result)
        print(len(result))
        self.assertEqual(list, type(result))

        print('\n---------- finder tests2 finished! -----------\n')
    def test_find_sub_network2(self):
        print('\n---------- Sub Network Finder tests 2 start -----------\n')

        from hdsubnetfinder.subnetwork.sub_network_finder import SubNetworkFinder
        import hdsubnetfinder.subnetwork.network_util as util
        from hdsubnetfinder.kernel.kernel_generator import KernelGenerator

        generator = KernelGenerator()
        small_kernel = generator.create_kernel(network_url=NETWORK_URL)
        small_sif = util.read_sif(file_url=NETWORK_URL)

        finder = SubNetworkFinder(network=small_sif, kernel=small_kernel)

        identifiers = ["NRAS", "KRAS", "MAPK1"]

        result = finder.get_sub_network(identifiers)
        self.assertIsNotNone(result)
        print(len(result))
        self.assertEqual(list, type(result))

        print('\n---------- finder tests2 finished! -----------\n')
Пример #7
0
    def test_find_sub_network(self):
        print('\n---------- Sub Network Finder tests start -----------\n')

        from hdsubnetfinder.subnetwork.sub_network_finder import SubNetworkFinder
        import hdsubnetfinder.subnetwork.network_util as util

        # Create kernel from pre-computed kernel file
        generator = KernelGenerator()
        small_kernel = generator.create_kernel_from_file(
            pre_computed_kernel_url=SAMPLE_KERNEL_URL)
        small_sif = util.read_sif(file_url=NETWORK_URL)

        finder = SubNetworkFinder(network=small_sif, kernel=small_kernel)

        identifiers = ["NRAS", "KRAS", "MAPK1"]

        result = finder.get_sub_network(identifiers)
        self.assertIsNotNone(result)

        print(len(result))

        self.assertEqual(list, type(result))

        print('\n---------- finder tests finished! -----------\n')
    def test_find_sub_network(self):
        print('\n---------- Sub Network Finder tests start -----------\n')

        from hdsubnetfinder.subnetwork.sub_network_finder import SubNetworkFinder
        import hdsubnetfinder.subnetwork.network_util as util


        # Create kernel from pre-computed kernel file
        generator = KernelGenerator()
        small_kernel = generator.create_kernel_from_file(pre_computed_kernel_url=SAMPLE_KERNEL_URL)
        small_sif = util.read_sif(file_url=NETWORK_URL)

        finder = SubNetworkFinder(network=small_sif, kernel=small_kernel)

        identifiers = ["NRAS", "KRAS", "MAPK1"]

        result = finder.get_sub_network(identifiers)
        self.assertIsNotNone(result)

        print(len(result))

        self.assertEqual(list, type(result))

        print('\n---------- finder tests finished! -----------\n')